Homology
similarity due to common ancestor
Synapamorphy
homologous trait no descendant has lost
Convergence
trait derived seperately
Homoplasy
happening independently
symplesiomorphy and convergence can lead to this
Symplesiomorphy
some descendants have lost trait
Bird and Bat wing Example
Synapamorphy in bats, not in birds
Lysosyme examples
convergent evolution in molecules
Molecules are homologous, ability is convergent
gene duplication event in different genes of the same family
monkeys, cows and Hoatzin: able to digest cellulose
Orthology
2 genes broke off in speciation event
Paralogy
2 genes broke off in a duplication event
Xenology
genes result of HGT
"true" alignment
when 2 sequences share more similarity than what we would expect by chance
Pairwise sequence alignment (PSA)
accounts for ins/del (gaps)
Make homology statements on DNA sequences
Multiple sequence alignment (MSA)
many
3 costs of making DNA alignments
cost of substitution (s)
cost of gap, gap penalty (w)
cost of extending a gap (g)
Progressive MSA
done in order, one by one
Iterative MSA
a little more complex, scoring to find best alignment
Stochastic MSA
evolutionary algorothims
ex. genetic algorithm ig